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1. Single-conformation spectroscopy of cold, protonated ^D PG-containing peptides: switching β-turn types and formation of a sequential type II/II′ double β-turn

   https://doi.org/10.1039/D1CP04852J  

   Lawler, John T.; Harrilal, Christopher P.; DeBlase, Andrew F.; Sibert, Edwin L.; McLuckey, Scott A.; Zwier, Timothy S. (January 2022, Physical Chemistry Chemical Physics)

   d -Proline ( D Pro, D P) is widely utilized to form β-hairpin loops in engineered peptides that would otherwise be unstructured, most often as part of a D PG sub-unit that forms a β-turn. To observe whether D PG facilitated this effect in short protonated peptides, conformation specific IR–UV double resonance photofragment spectra of the cold (∼10 K) protonated D P and L P diastereomers of the pentapeptide YAPGA was carried out in the hydride stretch (2800–3700 cm −1 ) and amide I/II (1400–1800 cm −1 ) regions. A model localized Hamiltonian was developed to better describe the 1600–1800 cm −1 region commonly associated with the amide I vibrations. The CO stretch fundamentals experience extensive mixing with the N–H bending fundamentals of the NH 3 + group in these protonated peptides. The model Hamiltonian accounts for experiment in quantitative detail. In the D P diastereomer, all the population is funneled into a single conformer which presented as a type II β-turn with A and D P in the i + 1 and i + 2 positions, respectively. This structure was not the anticipated type II′ β-turn across D PG that we had hypothesized based on solution-phase propensities. Analysis of the conformational energy landscape shows that both steric and charge-induced effects play a role in the preferred formation of the type II β-turn. In contrast, the L P isomer forms three conformations with very different structures, none of which were type II/II′ β-turns, confirming that L PG is not a β-turn former. Finally, single-conformation spectroscopy was also carried out on the extended peptide [YAA D PGAAA + H] + to determine whether moving the protonated N-terminus further from D PG would lead to β-hairpin formation. Despite funneling its entire population into a single peptide backbone structure, the assigned structure is not a β-hairpin, but a concatenated type II/type II′ double β-turn that displaces the peptide backbone laterally by about 7.5 Å, but leaves the backbone oriented in its original direction. 

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2. The Mutant β ^E202K Sliding Clamp Protein Impairs DNA Polymerase III Replication Activity

   https://doi.org/10.1128/JB.00303-21  

   Homiski, Caleb; Scotland, Michelle K.; Babu, Vignesh M.; Chodavarapu, Sundari; Maul, Robert W.; Kaguni, Jon M.; Sutton, Mark D. (November 2021, Journal of Bacteriology)

   Silhavy, Thomas J. (Ed.)

   ABSTRACT Expression of the Escherichia coli dnaN -encoded β clamp at ≥10-fold higher than chromosomally expressed levels impedes growth by interfering with DNA replication. We hypothesized that the excess β clamp sequesters the replicative DNA polymerase III (Pol III) to inhibit replication. As a test of this hypothesis, we obtained eight mutant clamps with an inability to impede growth and measured their ability to stimulate Pol III replication in vitro . Compared with the wild-type clamp, seven of the mutants were defective, consistent with their elevated cellular levels failing to sequester Pol III. However, the β E202K mutant that bears a glutamic acid-to-lysine substitution at residue 202 displayed an increased affinity for Pol IIIα and Pol III core (Pol IIIαεθ), suggesting that it could still sequester Pol III effectively. Of interest, β E202K supported in vitro DNA replication by Pol II and Pol IV but was defective with Pol III. Genetic experiments indicated that the dnaN E202K strain remained proficient in DNA damage-induced mutagenesis but was induced modestly for SOS and displayed sensitivity to UV light and methyl methanesulfonate. These results correlate an impaired ability of the mutant β E202K clamp to support Pol III replication in vivo with its in vitro defect in DNA replication. Taken together, our results (i) support the model that sequestration of Pol III contributes to growth inhibition, (ii) argue for the existence of an additional mechanism that contributes to lethality, and (iii) suggest that physical and functional interactions of the β clamp with Pol III are more extensive than appreciated currently. IMPORTANCE The β clamp plays critically important roles in managing the actions of multiple proteins at the replication fork. However, we lack a molecular understanding of both how the clamp interacts with these different partners and the mechanisms by which it manages their respective actions. We previously exploited the finding that an elevated cellular level of the β clamp impedes Escherichia coli growth by interfering with DNA replication. Using a genetic selection method, we obtained novel mutant β clamps that fail to inhibit growth. Their analysis revealed that β E202K is unique among them. Our work offers new insights into how the β clamp interacts with and manages the actions of E. coli DNA polymerases II, III, and IV. 

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3. Copper( ii ) ketimides in sp ³ C–H amination

   https://doi.org/10.1039/D1SC01990B  

   Jayasooriya, Isuri U.; Bakhoda, Abolghasem; Palmer, Rachel; Ng, Kristi; Khachemoune, Nour L.; Bertke, Jeffery A.; Warren, Timothy H. (December 2021, Chemical Science)

   Commercially available benzophenone imine (HNCPh 2 ) reacts with β-diketiminato copper( ii ) tert -butoxide complexes [Cu II ]–O t Bu to form isolable copper( ii ) ketimides [Cu II ]–NCPh 2 . Structural characterization of the three coordinate copper( ii ) ketimide [Me 3 NN]Cu–NCPh 2 reveals a short Cu-N ketimide distance (1.700(2) Å) with a nearly linear Cu–N–C linkage (178.9(2)°). Copper( ii ) ketimides [Cu II ]–NCPh 2 readily capture alkyl radicals R˙ (PhCH(˙)Me and Cy˙) to form the corresponding R–NCPh 2 products in a process that competes with N–N coupling of copper( ii ) ketimides [Cu II ]–NCPh 2 to form the azine Ph 2 CN–NCPh 2 . Copper( ii ) ketimides [Cu II ]–NCAr 2 serve as intermediates in catalytic sp 3 C–H amination of substrates R–H with ketimines HNCAr 2 and t BuOO t Bu as oxidant to form N -alkyl ketimines R–NCAr 2 . This protocol enables the use of unactivated sp 3 C–H bonds to give R–NCAr 2 products easily converted to primary amines R–NH 2 via simple acidic deprotection. 

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4. Spectroscopic and Theoretical Studies of Hg(II) Complexation with Some Dicysteinyl Tetrapeptides

   https://doi.org/10.1155/2021/9911474  

   Springfield, Elliot; Willis, Alana; Merle, John; Mazlo, Johanna; Ngu-Schwemlein, Maria (July 2021, Bioinorganic Chemistry and Applications)

   Osella, Domenico (Ed.)

   Tetrapeptides containing a Cys-Gly-Cys motif and a propensity to adopt a reverse-turn structure were synthesized to evaluate how O-, N-, H-, and aromatic π donor groups might contribute to mercury(II) complex formation. Tetrapeptides Xaa-Cys-Gly-Cys, where Xaa is glycine, glutamate, histidine, or tryptophan, were prepared and reacted with mercury(II) chloride. Their complexation with mercury(II) was studied by spectroscopic methods and computational modeling. UV-vis studies confirmed that mercury(II) binds to the cysteinyl thiolates as indicated by characteristic ligand-to-metal-charge-transfer transitions for bisthiolated S-Hg-S complexes, which correspond to 1 : 1 mercury-peptide complex formation. ESI-MS data also showed dominant 1 : 1 mercury-peptide adducts that are consistent with double deprotonations from the cysteinyl thiols to form thiolates. These complexes exhibited a strong positive circular dichroism band at 210 nm and a negative band at 193 nm, indicating that these peptides adopted a β-turn structure after binding mercury(II). Theoretical studies confirmed that optimized 1 : 1 mercury-peptide complexes adopt β-turns stabilized by intramolecular hydrogen bonds. These optimized structures also illustrate how specific N-terminal side-chain donor groups can assume intramolecular interactions and contribute to complex stability. Fluorescence quenching results provided supporting data that the indole donor group could interact with the coordinated mercury. The results from this study indicate that N-terminal side-chain residues containing carboxylate, imidazole, or indole groups can participate in stabilizing dithiolated mercury(II) complexes. These structural insights on peripheral mercury-peptide interactions provide additional understanding of the chemistry of mercury(II) with side-chain donor groups in peptides. 

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5. Correction: The role of energy cost on accuracy, sensitivity, specificity, speed and adaptation of T cell foreign and self recognition

   https://doi.org/10.1039/d1cp90136b  

   Shin, Gyubaek; Wang, Jin (July 2021, Physical Chemistry Chemical Physics)

   null (Ed.)

   Correction for ‘The role of energy cost on accuracy, sensitivity, specificity, speed and adaptation of T cell foreign and self recognition’ by Gyubaek Shin et al. , Phys. Chem. Chem. Phys. , 2021, 23 , 2860–2872, DOI: 10.1039/D0CP02422H. 

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